SMTL ID : 3ao2.1

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: C.16, H.18, E.43 Ligands: CD.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.16, A:H.18, A:E.43 CD.2: 6 residues within 4Å: Chain A: C.16, E.43, D.67 Ligands: CD.1, CL.3, MG.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.16, A:E.43, A:D.67, H2O.1, H2O.1 CD.9: 4 residues within 4Å: Chain B: C.16, H.18, E.43 Ligands: CD.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.16, B:H.18, B:E.43 CD.10: 5 residues within 4Å: Chain B: C.16, E.43, D.67 Ligands: CD.9, CL.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.16, B:E.43, B:D.67, H2O.3, H2O.3

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: C.16, L.25, E.43, D.67, N.71, F.72 Ligands: CD.2 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain B: C.16, L.25, E.43, D.67, N.71, F.72 Ligands: CD.10 Ligand excluded by PLIP

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: K.22, R.117, E.121, H.122, L.123 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.117, A:E.121, A:L.123 Water bridges: A:K.124 Salt bridges: A:K.22, A:H.122 SO4.5: 4 residues within 4Å: Chain A: C.16, T.17, H.18, K.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.18 Salt bridges: A:K.110 SO4.12: 5 residues within 4Å: Chain B: K.22, R.117, E.121, H.122, L.123 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.117, B:E.121, B:L.123 Water bridges: B:K.22, B:K.124 Salt bridges: B:K.22, B:H.122 SO4.13: 4 residues within 4Å: Chain B: C.16, T.17, H.18, K.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.17, B:H.18 Salt bridges: B:K.110

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.15, C.16, D.67 Ligands: CD.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.15, A:D.67

2 x AVX: 3-(7-bromo-1,3-benzodioxol-5-yl)-1-methyl-1H-pyrazol-5-amine(Non-covalent)

AVX.7: 13 residues within 4Å: Chain A: Y.34, W.59, N.135, H.136, R.138, S.146, G.148, E.149, V.152 Chain B: G.57, R.58, W.59, P.60 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.60, A:E.149 Halogen bonds: B:G.57 Hydrogen bonds: A:R.138, A:S.146 AVX.15: 14 residues within 4Å: Chain A: G.57, R.58, W.59, P.60, I.155 Chain B: Y.34, W.59, N.135, H.136, R.138, S.146, G.148, E.149, V.152 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.149, A:P.60 Hydrogen bonds: B:R.138, B:S.146 Halogen bonds: A:G.57

1 x DTV: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTV.8: 6 residues within 4Å: Chain A: T.44, G.45, Q.46, G.74, A.75, T.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.76 Water bridges: A:G.45, A:G.45, A:G.74, A:T.76

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.14: 6 residues within 4Å: Chain B: T.44, G.45, Q.46, G.74, A.75, T.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.75, B:T.76 Water bridges: B:G.74, B:G.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wielens, J. et al., Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1. Chemmedchem (2011)

Release Date

2011-03-16

Peptides

POL polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POL polyprotein

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